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Дата индексирования: Mon Oct 1 19:23:53 2012
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Geometrical core

Geometrical core

  

Alignment (example):

Distance spreading (Å)
 Minimal core size
 Bron – Kerbosch algorithm timeout (secs)
Alternative core new atoms (%)
 Cores count (0 for all)
 Superposition core identifier (0 for the main core)

Definitions

Alignment

An alignment of a set of structures is a set of positions, to each position some atoms from different structures correspond. In this service, only CA-atoms are included into alignments.

In a text representation of an alignment, all CA-atoms of the residues that are at the same position in different sequences form a position of the alignment (i.e., the first letters of the sequences form one position, the second ones — another position, etc.).

Geometrical core

Geometrical core is a subset of alignment positions those atoms are disposed similarly in all structures.

For any two positions, one may regard pairs of corresponding atoms: one pair for each structure. Difference between atom-to-atom distances in these pairs is the measure of similarity of the disposition.

Strictly speaking, a geometrical core is a subset of positions, such that 1) for any two of the positions, all corresponding atom-to-atom distances differ not more than the value of the parameter "Distance spreading"; and 2) it can not be extended without loss of the first feature.

Alternative cores

One alignment may contain more than one geometrical core. The largest of them is called the "main core". Different cores can include some common atoms.

 

Algorithm: Sergei Spirin, Andrei Alexeevski, Boris Nagaev
Programming: Boris Nagaev (computation), Sergei Spirin (web-interface)
Contact: sas@belozersky.msu.ru

The work was partly supported by the Russian Foundation for Basic Research, grant 09–04–92743

© S&S 2009